From 54ed7ea5e72d59e0f17db4893ecbaca3dfca151a Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 11 May 2015 21:33:40 +0000 Subject: Fixed gen_select_dataset so that it does not include Phenotype and Genotype groups when the corresponding data sets do not exist Interval Mapping no longer shows up for human traits Fixed the appearance of the mirror links on the main page --- wqflask/maintenance/gen_select_dataset.py | 52 +- .../new/javascript/dataset_menu_structure.json | 700 ++++----------------- wqflask/wqflask/templates/index_page.html | 12 +- .../templates/show_trait_mapping_tools.html | 118 ++-- 4 files changed, 216 insertions(+), 666 deletions(-) (limited to 'wqflask') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 694efeca..a2ad8c91 100755 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -35,7 +35,9 @@ from __future__ import print_function, division #config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') #print("cdict is:", cdict) -import our_settings +import sys +sys.path.append("/home/zas1024/") +import zach_settings import MySQLdb @@ -47,7 +49,7 @@ import urlparse from pprint import pformat as pf -#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI) +#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI) # build MySql database connection @@ -60,7 +62,7 @@ from pprint import pformat as pf def parse_db_uri(db_uri): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(our_settings.DB_URI) + parsed_uri = urlparse.urlparse(zach_settings.DB_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -104,12 +106,48 @@ def get_types(groups): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code - types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")] - types[species][group_name] += build_types(species, group_name) + #types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")] + if phenotypes_exist(group_name): + types[species][group_name] = [("Phenotypes", "Phenotypes")] + if genotypes_exist(group_name): + if group_name in types[species]: + types[species][group_name] += [("Genotypes", "Genotypes")] + else: + types[species][group_name] = [("Genotypes", "Genotypes")] + if group_name in types[species]: + types[species][group_name] += build_types(species, group_name) + else: + types[species][group_name] = build_types(species, group_name) return types +def phenotypes_exist(group_name): + print("group_name:", group_name) + Cursor.execute("""select Name from PublishFreeze + where PublishFreeze.Name = %s""", (group_name+"Publish")) + + results = Cursor.fetchone() + print("RESULTS:", results) + + if results != None: + return True + else: + return False + +def genotypes_exist(group_name): + print("group_name:", group_name) + Cursor.execute("""select Name from GenoFreeze + where GenoFreeze.Name = %s""", (group_name+"Geno")) + + results = Cursor.fetchone() + print("RESULTS:", results) + + if results != None: + return True + else: + return False + def build_types(species, group): """Fetches tissues @@ -196,7 +234,7 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - parse_db_uri(our_settings.DB_URI) + parse_db_uri(zach_settings.DB_URI) species = get_species() groups = get_groups(species) @@ -236,6 +274,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI)) + Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.DB_URI)) Cursor = Conn.cursor() main() diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index fabf3998..e790c9c0 100755 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -56,12 +56,6 @@ }, "barley": { "QSM": { - "Genotypes": [ - [ - "QSMGeno", - "QSM Genotypes" - ] - ], "Leaf mRNA": [ [ "B1LI0809R", @@ -79,12 +73,6 @@ "B1MI0809R", "Barley1 Leaf MOCK TTKS (Aug09) RMA" ] - ], - "Phenotypes": [ - [ - "QSMPublish", - "QSM Published Phenotypes" - ] ] }, "SXM": { @@ -113,13 +101,13 @@ "B30_K_1206_M", "Barley1 Leaf MAS 5.0 SCRI (Dec06)" ], - [ - "B30_K_1206_Rn", - "Barley1 Leaf gcRMAn SCRI (Dec06)" - ], [ "B30_K_1206_R", "Barley1 Leaf gcRMA SCRI (Dec06)" + ], + [ + "B30_K_1206_Rn", + "Barley1 Leaf gcRMAn SCRI (Dec06)" ] ], "Phenotypes": [ @@ -132,18 +120,6 @@ }, "drosophila": { "DGRP": { - "Genotypes": [ - [ - "DGRPGeno", - "DGRP Genotypes" - ] - ], - "Phenotypes": [ - [ - "DGRPPublish", - "DGRP Published Phenotypes" - ] - ], "Whole Body mRNA": [ [ "NCSU_DrosWB_LC_RMA_0111", @@ -152,18 +128,6 @@ ] }, "Oregon-R_x_2b3": { - "Genotypes": [ - [ - "Oregon-R_x_2b3Geno", - "Oregon-R_x_2b3 Genotypes" - ] - ], - "Phenotypes": [ - [ - "Oregon-R_x_2b3Publish", - "Oregon-R_x_2b3 Published Phenotypes" - ] - ], "Whole Body mRNA": [ [ "UAB_DrosWB_LC_RMA_1009", @@ -195,18 +159,6 @@ "GSE5281_RMA0709", "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" ] - ], - "Genotypes": [ - [ - "AD-cases-controlsGeno", - "AD-cases-controls Genotypes" - ] - ], - "Phenotypes": [ - [ - "AD-cases-controlsPublish", - "AD-cases-controls Published Phenotypes" - ] ] }, "AD-cases-controls-Myers": { @@ -229,12 +181,6 @@ "AD-cases-controls-MyersGeno", "AD-cases-controls-Myers Genotypes" ] - ], - "Phenotypes": [ - [ - "AD-cases-controls-MyersPublish", - "AD-cases-controls-Myers Published Phenotypes" - ] ] }, "Aging-Brain-UCI": { @@ -244,24 +190,12 @@ "GSE11882 UCI Human Entorhinal Cortex Affy U133 Plus2 (Sep13) RMA" ] ], - "Genotypes": [ - [ - "Aging-Brain-UCIGeno", - "Aging-Brain-UCI Genotypes" - ] - ], "Hippocampus mRNA": [ [ "UCI_HC_0913", "GSE11882 UCI Human Hippocampus Affy U133 Plus2 (Sep13) RMA" ] ], - "Phenotypes": [ - [ - "Aging-Brain-UCIPublish", - "Aging-Brain-UCI Published Phenotypes" - ] - ], "Postcentral Gyrus mRNA": [ [ "UCI_PCG_0913", @@ -282,18 +216,6 @@ "GSE15745 NIH Human Brain Cerebellum ILM humanRef-8 v2.0 (May10) RankInv" ] ], - "Genotypes": [ - [ - "Brain-Normal-NIH-GibbsGeno", - "Brain-Normal-NIH-Gibbs Genotypes" - ] - ], - "Phenotypes": [ - [ - "Brain-Normal-NIH-GibbsPublish", - "Brain-Normal-NIH-Gibbs Published Phenotypes" - ] - ], "Pons mRNA": [ [ "GSE15745-GPL6104_Po0510", @@ -314,12 +236,6 @@ ] }, "CANDLE": { - "Genotypes": [ - [ - "CANDLEGeno", - "CANDLE Genotypes" - ] - ], "Methylation": [ [ "CANDLE_Meth27_0313", @@ -344,12 +260,6 @@ ] }, "CEPH-2004": { - "Genotypes": [ - [ - "CEPH-2004Geno", - "CEPH-2004 Genotypes" - ] - ], "Lymphoblast B-cell mRNA": [ [ "UT_CEPH_RankInv0909", @@ -359,12 +269,6 @@ "Human_1008", "Monks CEPH B-cells Agilent (Dec04) Log10Ratio" ] - ], - "Phenotypes": [ - [ - "CEPH-2004Publish", - "CEPH-2004 Published Phenotypes" - ] ] }, "GTEx": { @@ -558,12 +462,6 @@ "GTEx Human Frontal Cortex (Apr14) RPKM" ] ], - "Genotypes": [ - [ - "GTExGeno", - "GTEx Genotypes" - ] - ], "Heart - Atrial Appendage mRNA": [ [ "GTEx_log2_HeartAt_0314", @@ -684,12 +582,6 @@ "GTEx Human Pancreas (Apr14) RPKM" ] ], - "Phenotypes": [ - [ - "GTExPublish", - "GTEx Published Phenotypes" - ] - ], "Pituitary Gland mRNA": [ [ "GTEx_log2_Pitui_0314", @@ -870,18 +762,6 @@ "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" ] ], - "Genotypes": [ - [ - "HBGeno", - "HB Genotypes" - ] - ], - "Phenotypes": [ - [ - "HBPublish", - "HB Published Phenotypes" - ] - ], "Prefrontal Cortex mRNA": [ [ "HBTRC-MLPFC_0611", @@ -920,12 +800,6 @@ ] }, "HCP": { - "Genotypes": [ - [ - "HCPGeno", - "HCP Genotypes" - ] - ], "Phenotypes": [ [ "HCPPublish", @@ -934,12 +808,6 @@ ] }, "HLC": { - "Genotypes": [ - [ - "HLCGeno", - "HLC Genotypes" - ] - ], "Liver mRNA": [ [ "HLC_0311", @@ -962,12 +830,6 @@ ] }, "HLT": { - "Genotypes": [ - [ - "HLTGeno", - "HLT Genotypes" - ] - ], "Lung mRNA": [ [ "GSE23546HLT0613", @@ -985,12 +847,6 @@ "GRNG-GSE23545HLT0613", "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" ] - ], - "Phenotypes": [ - [ - "HLTPublish", - "HLT Published Phenotypes" - ] ] }, "HSB": { @@ -1012,12 +868,6 @@ "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Genotypes": [ - [ - "HSBGeno", - "HSB Genotypes" - ] - ], "Hippocampus mRNA": [ [ "KIN_YSM_HIP_0711", @@ -1048,12 +898,6 @@ "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Phenotypes": [ - [ - "HSBPublish", - "HSB Published Phenotypes" - ] - ], "Posterior Inferior Parietal Cortex mRNA": [ [ "KIN_YSM_IPC_0711", @@ -1118,12 +962,6 @@ "INIA Macaca fasicularis Brain (Jan10) RMA **" ] ], - "Genotypes": [ - [ - "Macaca-fasicularisGeno", - "Macaca-fasicularis Genotypes" - ] - ], "Hippocampus mRNA": [ [ "INIA_MacFas_Hc_RMA_0110", @@ -1136,12 +974,6 @@ "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **" ] ], - "Phenotypes": [ - [ - "Macaca-fasicularisPublish", - "Macaca-fasicularis Published Phenotypes" - ] - ], "Prefrontal Cortex mRNA": [ [ "INIA_MacFas_Pf_RMA_0110", @@ -1163,19 +995,13 @@ "NCI_Agil_Mam_Tum_RMA_0409", "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], - [ - "MA_M_0704_R", - "NCI Mammary mRNA M430 (July04) RMA" - ], [ "MA_M_0704_M", "NCI Mammary mRNA M430 (July04) MAS5" - ] - ], - "Phenotypes": [ + ], [ - "AKXDPublish", - "AKXD Published Phenotypes" + "MA_M_0704_R", + "NCI Mammary mRNA M430 (July04) RMA" ] ] }, @@ -1225,13 +1051,13 @@ ] ], "Liver mRNA": [ - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], [ "LVF2_M_0704_M", "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" ] ], "Phenotypes": [ @@ -1243,10 +1069,6 @@ }, "B6D2F2": { "Brain mRNA": [ - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], [ "BRF2_M_0805_P", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" @@ -1256,16 +1078,20 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" ], [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" ], [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + "BRF2_M_0304_P", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], [ "BRF2_M_0304_M", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" + ], + [ + "BRF2_M_0304_R", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" ] ], "Genotypes": [ @@ -1273,12 +1099,6 @@ "B6D2F2Geno", "B6D2F2 Genotypes" ] - ], - "Phenotypes": [ - [ - "B6D2F2Publish", - "B6D2F2 Published Phenotypes" - ] ] }, "B6D2F2-PSU": { @@ -1305,32 +1125,14 @@ "PSU-B6D2F2_M2000812", "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200 **" ] - ], - "Phenotypes": [ - [ - "B6D2F2-PSUPublish", - "B6D2F2-PSU Published Phenotypes" - ] ] }, "B6D2RI": { - "Genotypes": [ - [ - "B6D2RIGeno", - "B6D2RI Genotypes" - ] - ], "Hippocampus mRNA": [ [ "UTHSC_B6D2RI_H_0912", "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **" ] - ], - "Phenotypes": [ - [ - "B6D2RIPublish", - "B6D2RI Published Phenotypes" - ] ] }, "BDF2-1999": { @@ -1345,12 +1147,6 @@ "UCLA_BDF2_LIVER_1999", "UCLA BDF2 Liver (1999) mlratio" ] - ], - "Phenotypes": [ - [ - "BDF2-1999Publish", - "BDF2-1999 Published Phenotypes" - ] ] }, "BDF2-2005": { @@ -1360,17 +1156,7 @@ "BDF2-2005 Genotypes" ] ], - "Phenotypes": [ - [ - "BDF2-2005Publish", - "BDF2-2005 Published Phenotypes" - ] - ], "Striatum mRNA": [ - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], [ "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" @@ -1378,33 +1164,37 @@ [ "SA_M2_0905_P", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + ], + [ + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "BHF2": { "Adipose mRNA": [ - [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], [ "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" ], + [ + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male mlratio" + ], [ "UCLA_BHF2_ADIPOSE_0605", "UCLA BHF2 Adipose (June05) mlratio" ] ], "Brain mRNA": [ - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], [ "UCLA_BHF2_BRAIN_FEMALE", "UCLA BHF2 Brain Female mlratio" ], + [ + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], [ "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" @@ -1417,38 +1207,32 @@ ] ], "Liver mRNA": [ - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], [ "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" ], + [ + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], [ "UCLA_BHF2_LIVER_0605", "UCLA BHF2 Liver (June05) mlratio" ] ], "Muscle mRNA": [ - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], [ "UCLA_BHF2_MUSCLE_FEMALE", "UCLA BHF2 Muscle Female mlratio **" ], + [ + "UCLA_BHF2_MUSCLE_MALE", + "UCLA BHF2 Muscle Male mlratio **" + ], [ "UCLA_BHF2_MUSCLE_0605", "UCLA BHF2 Muscle (June05) mlratio **" ] - ], - "Phenotypes": [ - [ - "BHF2Publish", - "BHF2 Published Phenotypes" - ] ] }, "BHHBF2": { @@ -1513,12 +1297,6 @@ "UCLA_BHHBF2_MUSCLE_FEMALE", "UCLA BHHBF2 Muscle Female Only" ] - ], - "Phenotypes": [ - [ - "BHHBF2Publish", - "BHHBF2 Published Phenotypes" - ] ] }, "BXD": { @@ -1603,14 +1381,14 @@ "UTHSC_BXD_WB_RNASeqtrim1112", "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 2.0" ], - [ - "UTHSC_BXD_WB_RNASeq1112", - "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed" - ], [ "UTHSC_BXD_WB_RNASeqtrim1_1112", "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 1.0" ], + [ + "UTHSC_BXD_WB_RNASeq1112", + "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed" + ], [ "UTHSC_BXD_WB_RNASeqEx1112", "UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM" @@ -1623,6 +1401,10 @@ "BR_U_1105_P", "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], + [ + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], [ "BR_U_0805_M", "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" @@ -1631,10 +1413,6 @@ "BR_U_0805_R", "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], [ "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" @@ -1745,10 +1523,6 @@ "Eye_M2_0908_R_ND", "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], - [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], [ "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA **" @@ -1757,6 +1531,10 @@ "Eye_M2_0908_R_WT", "Eye M430v2 WT Tyrp1 (Sep08) RMA **" ], + [ + "Eye_M2_0908_R_MT", + "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" + ], [ "DBA2J-ONH-1212", "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA" @@ -1961,15 +1739,15 @@ "MA_M2_0806_P", "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" ], - [ - "MA_M2_0706_P", - "Mouse Kidney M430v2 (Jul06) PDNN" - ], [ "MA_M2_0706_R", "Mouse Kidney M430v2 (Jul06) RMA" - ] - ], + ], + [ + "MA_M2_0706_P", + "Mouse Kidney M430v2 (Jul06) PDNN" + ] + ], "Leucocytes mRNA": [ [ "Illum_BXD_PBL_1108", @@ -1987,14 +1765,14 @@ ] ], "Liver Proteome": [ - [ - "EPFLETHZBXDprotHFD0514", - "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **" - ], [ "EPFLETHZBXDprotCD0514", "EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH **" ], + [ + "EPFLETHZBXDprotHFD0514", + "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **" + ], [ "EPFLBXDprotHFDRPN0214", "EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM **" @@ -2131,14 +1909,14 @@ ] ], "Neocortex mRNA": [ - [ - "DevNeocortex_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" - ], [ "DevNeocortex_ILM6.2P3RInv_1111", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" ], + [ + "DevNeocortex_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" + ], [ "HQFNeoc_1210v2_RankInv", "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" @@ -2151,13 +1929,13 @@ "HQFNeoc_0208_RankInv", "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], - [ - "DevNeocortex_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" - ], [ "DevNeocortex_ILM6.2P14RInv_1110", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" + ], + [ + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -2255,14 +2033,14 @@ "ONCRetILM6_0412", "ONC HEI Retina (April 2012) RankInv" ], - [ - "DoDTATRCRetMoGene2_1313", - "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA" - ], [ "DoDTATRCRetExMoGene2_1313", "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA Exon Level" ], + [ + "DoDTATRCRetMoGene2_1313", + "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA" + ], [ "ONCRetMoGene2_0413", "DoD TATRC Retina Affy MoGene 2.0 ST (Oct13) RMA **" @@ -2283,13 +2061,13 @@ "B6D2ONCILM_0412", "B6D2 ONC Retina (April 2012) RankInv **" ], - [ - "HEIONCvsCRetILM6_0911", - "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" - ], [ "G2HEIONCRetILM6_0911", "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" + ], + [ + "HEIONCvsCRetILM6_0911", + "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" ] ], "Spleen mRNA": [ @@ -2375,13 +2153,13 @@ "DevStriatum_ILM6.2P14RInv_1111", "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" ], - [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ], [ "DevStriatum_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" + ], + [ + "DevStriatum_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" ] ], "T Cell (helper) mRNA": [ @@ -2403,10 +2181,6 @@ ] ], "Ventral Tegmental Area mRNA": [ - [ - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" - ], [ "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" @@ -2414,6 +2188,10 @@ [ "VCUEtvsSal_0609_R", "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **" + ], + [ + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" ] ] }, @@ -2549,13 +2327,13 @@ ] ], "Hippocampus mRNA": [ - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], [ "HC_M2CB_1205_P", "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" + ], + [ + "HC_M2CB_1205_R", + "Hippocampus Consortium M430v2 CXB (Dec05) RMA" ] ], "Phenotypes": [ @@ -2572,12 +2350,6 @@ ] }, "HS": { - "Genotypes": [ - [ - "HSGeno", - "HS Genotypes" - ] - ], "Hippocampus mRNA": [ [ "OXUKHS_ILMHipp_RI0510", @@ -2604,18 +2376,6 @@ ] }, "HS-CC": { - "Genotypes": [ - [ - "HS-CCGeno", - "HS-CC Genotypes" - ] - ], - "Phenotypes": [ - [ - "HS-CCPublish", - "HS-CC Published Phenotypes" - ] - ], "Striatum mRNA": [ [ "OHSU_HS-CC_ILMStr_0211", @@ -2659,14 +2419,6 @@ "Hipp_Illumina_RankInv_0507", "Hippocampus Illumina (May07) RankInv" ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], [ "Illum_LXS_Hipp_NOE_1008", "Hippocampus Illumina NOE (Oct08) RankInv beta" @@ -2678,6 +2430,14 @@ [ "Illum_LXS_Hipp_NOS_1008", "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], + [ + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" + ], + [ + "Illum_LXS_Hipp_RSE_1008", + "Hippocampus Illumina RSE (Oct08) RankInv beta" ] ], "Phenotypes": [ @@ -2687,10 +2447,6 @@ ] ], "Prefrontal Cortex mRNA": [ - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], [ "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" @@ -2698,6 +2454,10 @@ [ "VCUEt_vs_Sal_0806_R", "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" + ], + [ + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" ] ] }, @@ -2735,13 +2495,13 @@ ] ], "Hippocampus mRNA": [ - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], [ "HC_M2_0606_MDP", "Hippocampus Consortium M430v2 (Jun06) RMA MDP" + ], + [ + "UMUTAffyExon_0209_RMA_MDP", + "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" ] ], "Liver mRNA": [ @@ -2774,12 +2534,6 @@ ] }, "NZBXFVB-N2": { - "Genotypes": [ - [ - "NZBXFVB-N2Geno", - "NZBXFVB-N2 Genotypes" - ] - ], "Mammary Tumors mRNA": [ [ "NCI_Mam_Tum_RMA_0409", @@ -2799,12 +2553,6 @@ "SOTNOT-OHSUGeno", "SOTNOT-OHSU Genotypes" ] - ], - "Phenotypes": [ - [ - "SOTNOT-OHSUPublish", - "SOTNOT-OHSU Published Phenotypes" - ] ] }, "Scripps-2013": { @@ -2817,29 +2565,11 @@ "ScrBXDACC4GEx0513", "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level **" ] - ], - "Genotypes": [ - [ - "Scripps-2013Geno", - "Scripps-2013 Genotypes" - ] - ], - "Phenotypes": [ - [ - "Scripps-2013Publish", - "Scripps-2013 Published Phenotypes" - ] ] } }, "rat": { "HSNIH": { - "Genotypes": [ - [ - "HSNIHGeno", - "HSNIH Genotypes" - ] - ], "Phenotypes": [ [ "HSNIHPublish", @@ -2915,18 +2645,6 @@ "UIOWA_Eye_RMA_0906", "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" ] - ], - "Genotypes": [ - [ - "SRxSHRSPF2Geno", - "SRxSHRSPF2 Genotypes" - ] - ], - "Phenotypes": [ - [ - "SRxSHRSPF2Publish", - "SRxSHRSPF2 Published Phenotypes" - ] ] } }, @@ -2946,12 +2664,6 @@ ] }, "J12XJ58F2": { - "Genotypes": [ - [ - "J12XJ58F2Geno", - "J12XJ58F2 Genotypes" - ] - ], "Phenotypes": [ [ "J12XJ58F2Publish", @@ -2962,12 +2674,6 @@ }, "tomato": { "LXP": { - "Genotypes": [ - [ - "LXPGeno", - "LXP Genotypes" - ] - ], "Phenotypes": [ [ "LXPPublish", @@ -3284,14 +2990,6 @@ }, "barley": { "QSM": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Leaf mRNA", "Leaf mRNA" @@ -3318,28 +3016,12 @@ }, "drosophila": { "DGRP": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Whole Body mRNA", "Whole Body mRNA" ] ], "Oregon-R_x_2b3": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Whole Body mRNA", "Whole Body mRNA" @@ -3348,24 +3030,12 @@ }, "human": { "AD-cases-controls": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Brain mRNA", "Brain mRNA" ] ], "AD-cases-controls-Myers": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3376,14 +3046,6 @@ ] ], "Aging-Brain-UCI": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Entorhinal Cortex mRNA", "Entorhinal Cortex mRNA" @@ -3402,14 +3064,6 @@ ] ], "Brain-Normal-NIH-Gibbs": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Cerebellum mRNA", "Cerebellum mRNA" @@ -3432,10 +3086,6 @@ "Phenotypes", "Phenotypes" ], - [ - "Genotypes", - "Genotypes" - ], [ "Methylation", "Methylation" @@ -3446,28 +3096,12 @@ ] ], "CEPH-2004": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Lymphoblast B-cell mRNA", "Lymphoblast B-cell mRNA" ] ], "GTEx": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Adrenal Gland mRNA", "Adrenal Gland mRNA" @@ -3658,14 +3292,6 @@ ] ], "HB": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Cerebellum mRNA", "Cerebellum mRNA" @@ -3683,10 +3309,6 @@ [ "Phenotypes", "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" ] ], "HLC": [ @@ -3694,38 +3316,18 @@ "Phenotypes", "Phenotypes" ], - [ - "Genotypes", - "Genotypes" - ], [ "Liver mRNA", "Liver mRNA" ] ], "HLT": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Lung mRNA", "Lung mRNA" ] ], "HSB": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Amygdala mRNA", "Amygdala mRNA" @@ -3794,14 +3396,6 @@ }, "macaque monkey": { "Macaca-fasicularis": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Amygdala mRNA", "Amygdala mRNA" @@ -3826,10 +3420,6 @@ }, "mouse": { "AKXD": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3880,10 +3470,6 @@ ] ], "B6D2F2": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3894,10 +3480,6 @@ ] ], "B6D2F2-PSU": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3908,24 +3490,12 @@ ] ], "B6D2RI": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Hippocampus mRNA", "Hippocampus mRNA" ] ], "BDF2-1999": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3936,10 +3506,6 @@ ] ], "BDF2-2005": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3950,10 +3516,6 @@ ] ], "BHF2": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -3976,10 +3538,6 @@ ] ], "BHHBF2": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" @@ -4232,10 +3790,6 @@ "Phenotypes", "Phenotypes" ], - [ - "Genotypes", - "Genotypes" - ], [ "Hippocampus mRNA", "Hippocampus mRNA" @@ -4250,14 +3804,6 @@ ] ], "HS-CC": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Striatum mRNA", "Striatum mRNA" @@ -4322,34 +3868,18 @@ "Phenotypes", "Phenotypes" ], - [ - "Genotypes", - "Genotypes" - ], [ "Mammary Tumors mRNA", "Mammary Tumors mRNA" ] ], "SOTNOT-OHSU": [ - [ - "Phenotypes", - "Phenotypes" - ], [ "Genotypes", "Genotypes" ] ], "Scripps-2013": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Anterior Cingulate Cortex mRNA", "Anterior Cingulate Cortex mRNA" @@ -4361,10 +3891,6 @@ [ "Phenotypes", "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" ] ], "HXBBXH": [ @@ -4402,14 +3928,6 @@ ] ], "SRxSHRSPF2": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ], [ "Eye mRNA", "Eye mRNA" @@ -4431,10 +3949,6 @@ [ "Phenotypes", "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" ] ] }, @@ -4443,10 +3957,6 @@ [ "Phenotypes", "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" ] ] } diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 5e0a92e3..cb29a07c 100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -206,12 +206,12 @@

GN1 Mirror and development sites

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 27504e51..bd1e6f1e 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -4,14 +4,16 @@
-
-
-
- -
- -
-
- -
- -
- -
-
- -
- -
- - -
-
- -
- -
- - -
-
-
-
- -
-
-
-
- -
+
@@ -211,7 +160,60 @@
- + {% if dataset.group.species != 'human' %} +
+
+
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ + +
+
+ +
+ +
+ + +
+
+
+
+ +
+
+
+
+ {% endif %} {% if dataset.group.species == 'human' %}